General

Sara telling Lavinia that she'd like to slap her, but won't because she wants to be the better person.
When Lavinia claims that Sara is lying to Lottie about what heaven is like, Sara concedes that she may not be right, but Lavinia will never see what heaven's like unless she starts being kinder to others- basically saying Lavinia is going to Hell.
As in the original story, Sara telling off Miss Minchin for claiming to be "kind" after everything she did to Sara, pointing out, "You are not kind, and this is not a home."
Mr. Carrisford, despite his poor health and limited information, sets out to find his good friend's daughter, and eventually succeeds.
In the end, when it turns out that Sara is wealthy again, Miss Minchin tries to appeal to her, but Sara sees right through her lies and tells her that while she is grateful for some of the things Miss Minchin did for her, she will never let Miss Minchin hurt her again.

Route-specific

On Becky's route, Lavinia's cat Tybalt escapes, and Becky and Sara have to find him, tracking him to the tower of the church. Becky nearly falls to her death, but Sara grabs hold of her hand, convinces her to not let go and holds on long enough for the tower keeper to get there.
On Ermengarde's route, Ermengarde, whom most of her schoolmates thought of as fat, dimwitted and clumsy, manages to covertly slip Sara a bit of food under Miss Minchin's nose.